Chapter 4:
PROKARYOTIC DIVERSITY
3. Gram-negative and Phototropic Non-Proteobacteria
2. Proteobacteria
1. Prokaryote Habitats, Relationships & Biomes
4. Gram-Positive Bacteria
5. Deeply Branching Bacteria
6. Archaea
1. Prokaryote Habitats,
Relationships & Biomes
Important Metabolic Terminology
Oxygen tolerance/usage:
aerobic – requires or can use oxygen (O2)
anaerobic – does not require or cannot tolerate O2
Energy usage:
phototroph – uses light as an energy source
• all photosynthetic organisms
chemotroph – acquires energy from organic or inorganic molecules
• organotrophs – get energy from organic molecules
• lithotrophs – get energy from inorganic molecules
…more Important Terminology
Facultative vs Obligate (or Strict):
facultative – “able to, but not requiring”
• e.g., facultative anaerobes can survive w/ or w/o O2
obligate – “absolutely requires”
• e.g., obligate anaerobes cannot survive in O2
Carbon Source:
autotroph – uses CO2 as a carbon source
• e.g., photoautotrophs or chemoautotrophs
heterotroph – requires an organic carbon source
• e.g., chemoheterotroph – gets energy & carbon from organic molecules
Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs
Symbiotic Relationships
Symbiotic relationships (close, direct interactions) between
different organisms in nature are of several types:
• e.g., humans have beneficial
bacteria in their digestive
tracts that also benefit from
the food we eat (mutualism)
Microbiomes
All the microorganisms that inhabit a particular organism
or environment (e.g., human or soil microbiome):
Classification in the Bacterial Domain
We will look at important genera from a variety of bacterial groups
classified largely on staining & rRNA sequences (ribotyping):
Gram-negative Bacteria
• Proteobacteria
• Nonproteobacteria & Phototrophic Bacteria
Gram-positive Bacteria
• High G+C (Actinobacteria)
• Low G+C (Firmicutes)
Deeply Branching Bacteria
2. Proteobacteria
Alphaproteobacteria
Betaproteobacteria
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
Alphaproteobacteria
Pathogenic genera:
Rickettsia
Chlamydia
Rhizobium
• intracellular pathogens
• typhus, Rocky Mountain spotted fever
• C. trachomatis – most common STD
Most are oligotrophs:
• nitrogen fixation in soil
R. rickettsii
Rhizobium
Betaproteobacteria
Pathogenic genera:
Neisseria
Thiobacillus
Bordetella
• oxidize H2S to sulfate is soil
• important in sulfur cycle
• gonorrhea (N. gonorrheae)
• whooping cough (B. pertussis)
• meningococcal meningitis
(N. meningitidis)
N. meningitidis
Most are eutrophs:
Gammaproteobacteria
Escherichia
Pseudomonas
Salmonella
Largest & most diverse class of Proteobacteria, including many
enteric bacteria and human pathogens:
• E. coli
• opportunistic pathogens
• typhoid fever, foodborne
salmonellosisL. pneumophila
Vibrio
• cholera (V. cholerae)
Legionella
• legionnaires disease (L. pneumophila)
Deltaproteobacteria
Small class of Proteobacteria containing soil bacteria that
reduce sulfate (Desulfovibrio) and the Myxobacteria that form
unusual “fruiting bodies”:
Myxobacteria
Epsilonproteobacteria
Pathogenic genera:
Helicobacter
Campylobacter
• H. pylori – peptic ulcers
• various species cause
blood poisoning, intestinal
illness (e.g., C. jejuni)H. pylori
Smallest class of Proteobacteria containing microaerophilic
species that are typical helical or vibrioid in shape :
3. Gram-Negative & Phototropic
Non-Proteobacteria
Spirochetes
Treponema
Borrelia
• T. pallidum – syphilis
• B. burgdorferi – Lyme disease
Very thin, highly coiled bacteria
that are hard to see under the
microscope and harder to
culture:
The CFB Group
Grouped based on DNA similarity and includes the following
genera:
Cytophaga Fusobacterium Bacteroides
Bacteroides
• Some are potentially
pathogenic (Cytophaga,
Fusobacterium), others are
beneficial (Bacteroides)
• most are anaerobic rods
Sheath
Vegetativecell
Heterocyst
Akinete
Anabaena Oscillatora
Cyanobacteria
Gram-negative, oxygenic photoautotrophs
Anabaena
• carry out nitrogen fixation in non-photosynthetic heterocysts
• produce vast amounts of oxygen gas via photosynthesis, fix nitrogen (N2 NH4+)
Purple & Green Bacteria
Obligately anaerobic, anoxygenic photoautotrophs
• use organic molecules as a source of electrons (not H2O)
Green and Purple non-sulfur bacteria
Green and Purple sulfur bacteria
• use H2S as a source of electrons
• elemental sulfur is then released
(green sulfur bacteria) or forms
inclusions (purple sulfur bacteria)
4. Gram-Positive Bacteria
Classification of Gram-Positive Bacteria
Gram-positive bacteria are grouped based on DNA similarity:
Low G+C Gram-positive bacteria (Firmicutes)
• contains many serious pathogens
• characterized by branching filaments
High G+C Gram-positive bacteria (Actinomycetes)
• includes some pathogens
Actinobacteria (High G+C)
Streptomyces
Corynebacterium
Mycobacterium
• important soil bacteria, recycle nutrients
• many produce antibiotics (erythromycin, tetracycline)
• diphtheria (C. diphtheria)
• tuberculosis (M. tuberculosis), leprosy (M. leprae)
• contain mycolic acids in cell wall (stain acid-fast)
Bifidobacterium
• significant member of beneficial gut microbiota
C. diphtheria
Streptomyces
Firmicutes (Low G+C)…
Streptococcus
Staphylococcus
*Bacillus
*Clostridium *produce
endospores
• strep throat (S. pyogenes)
• MRSA (S. aureus)
• anthrax (B. anthracis)
• tetanus (C. tetani)
• botulism (C. botulinum)
C. difficile
S. pyogenes
S. aureus
• colitis (C. difficile)
Mycoplasma
• very small (less than 1 mm)
Lactobacillus
…more Firmicutes
• species used in fermented food products (e.g., yogurt, buttermilk, pickles)
• part of normal, healthy microbiota in human mouth, digestive tract, vagina
• no cell wall (stain Gram-negative)
• obligate intracellular pathogens
Mycoplasma
colonies
5. Deeply Branching Bacteria
Last Common Universal Ancestor
What Are “Deeply Branching Bacteria”?
Bacteria very close
to the base of the
phylogenetic tree:
• members of the
domain Bacteria
that diverged
very early, ~3.5
billion years ago
Genera of “Deeply Branching Bacteria”
Acetothermus
• deepest branching bacteria known to date
• thermophiles and hyperthermophiles
Aquifex
• adapted to harshest conditions on planet
(e.g., thermal oceanic vents that reach 138oC!)
Deinococcus
• D. radiodurans known as “Conan the
Bacterium” for the extremes of heat, UV,
radioactivity, etc, it can survive
D. radiodurans
6. Archaea
The Domain Archaea
Highly diverse group of prokaryotes first classified in 1977 by
Carl Woese and George Fox:
• cell walls made of material other than peptidoglycan
• have unusual membrane lipids
• much larger genomes that bacteria
• have metabolic processes, rRNA sequences and other features
more closely resembling eukaryotes
• e.g., initiate translation with methionine (as do eukaryotes) rather
than N-formyl methionine as do the Bacteria
Two Main Phyla
Crenarchaeota
• most are hyperthermophiles, some
acidophiles
Euryarchaeota
• includes the methanogens, halophiles, a few
thermophiles
**NO known archaeon causes disease in humans or animals!**
Other Phyla
• Korarchaeota, Nanoarchaeota, Thaumarchaeota
• based on environmental RNA
Sulfolobus
Key Terms for Chapter 4
• autotroph, heterotroph, oligotroph, eutroph
• facultative vs obligate
• aerobic vs anaerobic
• thermophile, halophile
• phototroph, chemotroph, organotroph, lithotroph
• symbiosis: mutualism, amensalism, commensalism,
neutralism, parasitism